Re: [galaxy-dev] Tool Shed packages for BLAST+ binaries
Hi Simon, Further to our discussion here: http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-August/016310.html http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-August/016316.html Simon wrote: An example is the NCBI BLAST+ suite, which failed to build on my (EL6) system, because it couldn't run /usr/bin/touch. That's pretty dumb, and pretty simple to solve in isolation - it needs to be running /bin/touch instead. This was an oddity in the NCBI compile scripts for BLAST 2.2.26+ which can be avoided via a symlink, editing their code, or more simply just downloading their provided binaries. I prefer the later because it is simpler, faster, and should better ensure reproducibility by eliminating things like different compilers and their settings. Unfortunately the new install process to do this from within the Tool Shed is glitching on the Tool Shed's nightly tests: On Tue, Aug 27, 2013 at 2:18 PM, Dave Bouvier d...@bx.psu.edu wrote: Peter, I also tried running the command that returns error code 64 on the same system that runs the automated tests, and it downloaded the correct file for that operating system and architecture. So I'm not sure why it's failing when run through buildbot, but I'll look into it and get back to you. I've added a trello card to track progress on this issue: https://trello.com/c/9ERDMc7j/1079-toolshed-investigate-cause-of-shell-commands-failing-through-buildbot-when-they-are-valid-commands --Dave B. Nevertheless, the simple binary install is working for me and Bjoern. Could you try the Test Tool Shed package and let us know if that works for you? Test Tool Shed, http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus depends on this, http://testtoolshed.g2.bx.psu.edu/view/iuc/package_blast_plus_2_2_26 Or, try installing this directly (although it won't get used yet): http://toolshed.g2.bx.psu.edu/view/iuc/package_blast_plus_2_2_26 Given some confirmation then I think I will update the Main Tool Shed http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus (which currently tries to compile BLAST) to instead depend on the new package which fetches the binaries. Thanks, Peter ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Local installation: Uploading fastq file takes ages - why?
Hi Nate, Thanks for your reply. Both debug and use_interactive are set to true in my universe_wsgi.ini. However, I discovered a short while after sending the message that uploading the gzipped files made the process very fast. Obviously it's a clear short sight on my part, sorry. Regards, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 From: Nate Coraor [n...@bx.psu.edu] Sent: Thursday, August 29, 2013 5:07 PM To: בעז שאנן Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Local installation: Uploading fastq file takes ages - why? On Aug 14, 2013, at 8:39 AM, Boaz Shaanan wrote: Hi, On my local galaxy installation (updated to the latest version yesterday), it takes ages (hours!) to upload a fastq files. I attach a report from the the computer on which galaxy is installed. The fastq file is uploaded from 132.72.88.186. Initially there is an error message (the attached file also includes the debug url at the end) and after a while the upload proceeds but takes very long time. Transferring the file by sftp between the two computers takes only seconds. Is there anytning wrong with my installation (i.e. something is not properly defined or something like this). Hi Boaz, Could you make sure that debug and use_interactive are both set to False in universe_wsgi.ini? Thanks, --nate I'd appreciate your help. Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 galaxy_local_server_error.txt___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] August 2013 Galaxy Update Newsletter is out
Hello all, The September 2013 Galaxy Update is hot off the presshttp://wiki.galaxyproject.org/GalaxyUpdates/2013_09: - A record *five new public servershttp://wiki.galaxyproject.org/GalaxyUpdates/2013_09#New_Public_Servers * - 30 new papershttp://wiki.galaxyproject.org/GalaxyUpdates/2013_09#New_Papers - Take the 2014 Galaxy Training Surveyhttp://wiki.galaxyproject.org/GalaxyUpdates/2013_09#A2014_Galaxy_Training_Survey - Open Positionshttp://wiki.galaxyproject.org/GalaxyUpdates/2013_09#Who.27s_Hiringat six different organizations - Upcoming Eventshttp://wiki.galaxyproject.org/GalaxyUpdates/2013_09#Eventsincluding training in California, Sydney, Italy, Toulouse, and Boston. - Aug 12, 2013 Galaxy Distributionhttp://wiki.galaxyproject.org/GalaxyUpdates/2013_09#Aug_12.2C_2013_Galaxy_Distribution - Tool Shed Contributionshttp://wiki.galaxyproject.org/GalaxyUpdates/2013_09#Tool_Shed_Contributions - Other Newshttp://wiki.galaxyproject.org/GalaxyUpdates/2013_09#Other_News If you have anything you would like to see in the next *Galaxy Updatehttp://wiki.galaxyproject.org/GalaxyUpdates *, please let us know. Dave Clements and the Galaxy Team -- http://galaxyproject.org/GCC2013 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
